Fifteen years ago, a Muslim scholar, a Christian priest and a Jewish philanthropist came together in London to create Three Faiths Forum (3FF), a platform for community leaders to engage with each another and break down barriers. But today, some of the most valuable work the charity undertakes is in schools, ensuring that tensions between faith communities don't trickle down to the next generation.

Often this will simply be making sure that children of different faiths have an opportunity to meet one another or addressing a lack of knowledge about other religions; occasionally more severe problems occur. "We're contacted by RE teachers to help when there's been anti-Jewish, -Muslim or -Christian sentiment," says Debbie Danon, the charity's education manager.

Deputy director Rachel Heilbron speaks of one particularly serious case they became involved with last year. A teacher discussing the features of a church with a group of 14-year-old students at a non-denominational school in London mentioned synagogues. Some of the students complained they didn't want to learn about "Jew stuff". They said that Jews were dirty and smelly and that they kept money under their hats. As the situation escalated, some of the children began banging on the tables, chanting: "Kill the Jews, kill the Jews."

One teacher at the school was worried the shocking incident had not been adequately dealt with, and that staff had tried to ignore it, hoping it would disappear by itself. "These are problems for everyone and they're not prioritised," Danon explains. "Senior management pushes it to the backburner and it's seen as the responsibility of the RE teacher to sort out," says Danon. But a report into the effectiveness of religious education presented by researchers at the University of Glasgow this year found that RE teachers felt under-confident, under-valued and under increasing pressure to "teach to the test" at the expense of tackling real faith issues.

One solution the charity has found is to link schools together, enabling pupils of different faiths to meet and exchange information about one another – an opportunity they might not otherwise have. At a linking event between La Sainte Union and Islamia schools this month, part of 3FF's 15th birthday celebrations, Catholic and Muslim children told me they kept in touch with each other in between sessions using Facebook and BlackBerry Messenger. "Every school should do this," one said.

During another event at Ayesha Community Education in north London, 16-year-old Mariam Rafi said: "I've come across people who say, 'You're Muslim, you're Afghan, you must be a terrorist' and it's just reassuring finding out that most people are open-minded … I'm excited to get together with people of other faiths, to let them know that we want to be friends."

A key problem, says Danon, is that faith schools often don't have the staff to teach about other faiths. Textbooks used to teach RE are sometimes out of date and don't really get to the root of the problem – "you can't ask a book questions", as one student put it. But faith schools at least provide an encouraging environment for children to explore and express their religion. Elsewhere, Danon has come across children who wouldn't even own up to being religious until 3FF came along. "They never felt safe enough," she says. "In schools where students are all from different backgrounds and beliefs, they don't interact intentionally about what they believe, and if they do it turns into an argument."

While 9/11 pushed the issue of interfaith relations up the agenda, many of the children the charity works with are too young to know or understand what happened that day. Nonetheless, the community tensions are evident. 3FF runs a session called "The Art of Asking" where children are encouraged to ask anything they want about other faiths. "Why do Christians think they're superior to everyone else?", "Why do Muslims fast before they bomb people?" and "Why are Jews always trying to conquer Muslims?" are all questions that have come up.

The charity's emphasis is on the value of dialogue, as opposed to debate. Debate implies that one side is right and the other wrong. In contrast, teaching children to have an open dialogue with one another means they can understand and respect each other's beliefs while maintaining their own values. They discover a more sensitive, thoughtful and positive vocabulary to discuss these issues with.

While talking at the linking event, the headmistresses of La Sainte Union and Islamia schools agreed that the value of 3FF's work lay in its acknowledgement of both our similarities and our differences; allowing children of different faiths to recognise their similarities without losing their own tradition.

As Danon puts it: "It's about showing them that they're similar, not telling them they're all the same."